To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CompGO")

In most cases, you don't need to download the package archive at all.

CompGO

   

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see CompGO.

An R pipeline for .bed file annotation, statistical comparison of GO term enrichment between gene sets and data visualisation

Bioconductor version: 3.3

This package contains functions to accomplish several tasks. It is able to download full genome databases from UCSC, import .bed files easily, annotate these .bed file regions with genes (plus distance) from aforementioned database dumps, interface with DAVID to create functional annotation and gene ontology enrichment charts based on gene lists (such as those generated from input .bed files), statistically compare gene ontology enrichment between multiple experiments and finally visualise and compare these enrichments using directed acyclic graphs or scatterplots. CompGO also enables clustering of experiments based on their GO profiles and provides functions for performing and visualising principle component analysis.

Author: Sam D. Bassett [aut], Ashley J. Waardenberg [aut, cre]

Maintainer: Ashley J. Waardenberg <awaardenberg at cmri.org.au>

Citation (from within R, enter citation("CompGO")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CompGO")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CompGO")

 

PDF CompGO-vignette.pdf
PDF R Script Introduction
PDF   Reference Manual
Text   NEWS

Details

biocViews GO, GeneSetEnrichment, MultipleComparison, Software, Visualization
Version 1.8.1
In Bioconductor since BioC 2.14 (R-3.1) (2.5 years)
License GPL-2
Depends RDAVIDWebService
Imports rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source CompGO_1.8.1.tar.gz
Windows Binary CompGO_1.8.1.zip
Mac OS X 10.9 (Mavericks) CompGO_1.8.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CompGO/tree/release-3.3
Package Short Url http://bioconductor.org/packages/CompGO/
Package Downloads Report Download Stats

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